Projects

Inferring Kinetic Models for Large-Scale Biochemical Networks

Lead Institution

University of Washington

Principal Investigator

Herbert Sauro

Project type

Large-Scale EMSL Research

Mechanistic models of cell networks that accurately predict changes in input-output dynamics and outcomes upon perturbation have the potential to facilitate a greater understanding of the…

Plant proteome structure-function and pKa prediction augmented with environmental considerations, Deep Learning and integrated datasets

Lead Institution

Johns Hopkins University

Principal Investigator

Carolyn Fitch

Project type

Large-Scale EMSL Research

One of the goals of computational biology is to model cellular behavior. At the crux of this endeavor is the need to understand proteins in their biologically relevant environmental context. In other…

Revealing oxalate-mediated carbon flow through plant-fungal-bacterial rhizosphere interactions as part of a globally important carbon-sequestering biogeochemical process

Lead Institution

Los Alamos National Laboratory

Principal Investigator

Buck Hanson

Project type

Large-Scale EMSL Research

Bacterial and fungal interactions in plant rhizospheres impart a myriad of beneficial functions to plant and soil health as well as playing important roles in biogeochemical cycling. However, the…

Determination of the Molecular Architecture and Temporal Dynamics that Drive Microbial Lignocellulose Degradation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Song Feng

Project type

Large-Scale EMSL Research

In order to link phenotypic outcomes to molecular determinants, we have developed an integrated functional profiling platform, PhenoProfiling, that pairs activity-based probes (ABPs) with…

The knowns against the unknowns: Photosynthesis gene discovery through multi-omic survey of photosynthetic mutants during light stress

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Setsuko Wakao

Project type

Large-Scale EMSL Research

To advance genome-based understanding of photosynthesis, we have generated a high-quality, phenotyped photosynthesis mutant library in the model unicellular green alga, Chlamydomonas reinhardtii…

Numerical Modeling of Hydrologic Exchange and Biogeochemistry in Dynamic Rivers

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Timothy Scheibe

Project type

Large-Scale EMSL Research

The River Corridor SFA project (https://www.pnnl.gov/projects/river-corridor) uses a ModEx (integrated models and experiments) approach to study hydrologic exchange fluxes (HEFs) between river…

Disentangling the impacts of particle mixing state on ice nucleation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Susannah Burrows

Project type

Large-Scale EMSL Research

Atmospheric ice nucleating particles (INPs) are rare particles required to initiate freezing in clouds at temperatures warmer than ca. -38°C, and therefore can have significant impacts on weather and…

Determining mechanisms and rates of microbial plastic biodegradation and the consequences for freshwater carbon cycling

Lead Institution

University of Michigan

Principal Investigator

Melissa Duhaime

Project type

Large-Scale EMSL Research

In recent years, plastic litter has been documented in widespread and diverse marine, freshwater, and even aeolian biomes. It is estimated that 4.8-12.7 million tons of plastics enters the ocean in a…

Coupling X-ray Computed Tomography images with ModEx inspired laboratory manipulation experiment for predicting greenhouse gas fluxes from Terrestrial-Aquatic Interfaces

Lead Institution

Emory University

Principal Investigator

Debjani Sihi

Project type

Large-Scale EMSL Research

The Terrestrial Aquatic Interfaces (TAIs) with dynamic hydrological exchange represent the most biogeochemically active and diverse systems. Frequent hydrological oscillations due to tidal…

Novel AI approach to unravel complex protein folding landscapes: towards better bioeconomy

Lead Institution

Chalmers University of Technology

Principal Investigator

Pernilla E L Wittung-Stafshede

Project type

Large-Scale EMSL Research

Many proteins, especially enzymes, need to bind metal ion cofactors, or gain other posttranslational modifications (PTM), to be active. None of these processes are static; protein structures are…

Developing the proteome network regulating structure and function of root-development of switchgrass on marginal lands

Lead Institution

Tennessee State University

Principal Investigator

Suping Zhou

Project type

Large-Scale EMSL Research

Abstract: Switchgrass (Panicum virgatum) is a leading biomass perrenial grass native to the United States. Switchgrass plants are known for tolerance of poor soil conditions, mainly due to its…

Uncovering dynamic changes in metabolism and signaling across cell types in the Sorghum bicolor stem using multiomics

Lead Institution

University of Illinois at Urbana-Champaign

Principal Investigator

Amy Marshall-Colon

Project type

Large-Scale EMSL Research

Sorghum bicolor is an important bioenergy crop because it has high nutrient and water use efficiency, and produces a large quantity of biomass that can be processed into ethanol for biofuels. Many…

Transformations of organic coatings in light-absorbing aerosols released by biomass burning, and associated impacts on the interactions with clouds

Lead Institution

Michigan Technological University

Principal Investigator

Claudio Mazzoleni

Project type

Large-Scale EMSL Research

We propose to employ the unique analytical capabilities at EMSL to study samples collected during ongoing ASR DOE-funded projects. The goal is to study the interactions of black carbon-containing…

Single Particle Characterization for Interpreting Ice Nucleating Particle Measurements in the SAIL Field Study

Lead Institution

Colorado State University

Principal Investigator

Paul Demott

Project type

Large-Scale EMSL Research

Ice formation in clouds is a process that is still not fully understood, yet critically affects precipitation, cloud lifetime, and the radiation balance. Mixed-phase clouds in the Western U.S…

Illuminating emergent properties underlying complex carbon degradation within communities of soil microorganisms

Lead Institution

University of Pittsburgh

Principal Investigator

Erik Wright

Project type

Large-Scale EMSL Research

Soil microorganisms play a key role in the global carbon cycle by degrading the complex carbon molecules comprising plant litter and cell detritus. This provides a critical ecosystem service by…

Probing Atmospheric Nanoplastics: An Unrecognized Urban Source of Airborne Particles

Lead Institution

Purdue University

Principal Investigator

Alexander Laskin

Project type

Large-Scale EMSL Research

fragments of microplastic or larger plastic debris discharged into terrestrial and aquatic environments, while atmospheric occurrence of EnvNP is solely attributed to aerosolization by wind and other…

The thiol redox proteome dynamics in Arabidopsis thaliana in response to light

Lead Institution

Universidad de Sevilla

Principal Investigator

Francisco Javier Cejudo

Project type

Large-Scale EMSL Research

Plant performance relies on regulatory mechanisms that allow the rapid adaptation of their metabolism to light, the key stimulus for growth and development of photosynthetic organisms. Thus, dark…

Unraveling the biochemical and metabolic networks controlling bacterial cellulose biosynthesis

Lead Institution

University of Kentucky

Principal Investigator

Kendall Corbin

Project type

Large-Scale EMSL Research

Synthetic biology is a rapidly evolving field that uses novel engineering approaches to enhance the capabilities of organisms. Cellulose producing bacteria with commercial value, such as many in the…

Computational Mechanistic Studies of Methyl-coenzyme M Reductase Enzyme

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Bojana Ginovska

Project type

Large-Scale EMSL Research

Methane is the second most abundant greenhouse gas after CO2, which accounts for 14% of global greenhouse gas emissions, and it is by far the largest constituent of natural gas deposits. Methyl…

Identification of Individual Particle Chemical Composition, Morphology, and Ice Nucleation Properties in the Arctic

Lead Institution

University of Michigan

Principal Investigator

Kerri Pratt

Project type

Large-Scale EMSL Research

The proposed project will address critical gaps in our understanding of the Arctic aerosol chemical composition, mixing state, sources, and ice nucleation properties through chemical imaging and ice…